Dominika is entirely correct, the F and (especially) sigma(F) values
are clearly inconsistent with my naive suggestion that columns could
have been swapped accidentally in an mtz file.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D
On Thu, 16 Aug 2007, Clemens Vonrhein wrote:
Maybe we should contact Google to let them do it for us ;-)
Better yet, simply download your images to a computer that uses AT&T as an
internet service provider. All the information will be automatically
copied and stored by the NSA
A small, but very important excerpt from the original Randy Read's message
"... Nature did not allow us to use the word "fabricated". Nor were we
allowed to discuss other structures from the same group, if they weren't
published in Nature."
So, are there OTHER SUSPECT STRUCTURES from the same
For the purposes of evaluating a manuscript, the editorial policy of NSMB
explicitly states that the atomic coordinates and structure factors files
should be provided to reviewers and editors upon request, if those are not
already freely accessible in a publicly available and recognized database.
h
No one knows definitively if this was fabricated.
Well, at least one person does.
But I agree, it is important to keep in mind that the proper venue for
determining guilt or innocence in the case of fraud is the court system.
Until fairly recently, the idea of presumed innocence and the
Nature DOES require availability of structure factors and coordinates as
a matter of policy, and also to make them available for review on demand.
If the reviewer does not want them, the editor can't do anything about.
One also cannot demand of a biologist reviewer to reconstruct
maps, but others
A comment from my collaborator's student suggests a partial
answer. This afternoon he happened to say "but of course the
reviewers will look at the model, I just deposited it!". He was
shocked to find that "hold for pub" means that even reviewers can't
access the data. Can that be changed?
I like to emphasize that the infamous table 1 alone should
have immediately tipped off any competent reviewer.
The last shell I/Isig is 1.3 and rmerge 0.11 (!).
And keep in mind that this statistics comes from
merging data from FOUR different crystals! (That's
clearly and unambigously stated in
Due to these recent, highly publicized irregularities and ample
(snide) remarks I hear about them from non-crystallographers, I am
wondering if the trust in macromolecular crystallography is beginning
to erode. It is often very difficult even for experts to distinguish
fake or wishful think
Ok, enough political (in)correctness. Irrespective of fabricated or not,
I think this points to a general problem of commercial journals and
their review process, as it seems that selling (.com) hot stuff
induces an extraordinary capability of denial.
The comment, as someone noted, does not addr
A few thoughts following on Richard Baxter and George Sheldrick . . .
Re: gaps in the lattice see the tyr-tRNA synthase structures (1tya for
example). Fersht has written a whole book full of insights from these
structures.
Re: Phaser Z scores. For some MR work with two xtal forms of a str
There are several issues under current discussion. We
outline a few of these below, in order of importance.
The structure 2hr0 is unambiguously fake. Valid arguments
have already been published in a Brief Communication by
Janssen et. al (Nature, 448:E1-E2, 9 August 2007). However,
the publish
Dear all
Personally I feel that we really have an obligation to make the raw images
available, even if it is painful to do so in terms of data storage. It is the
only way of truly allowing others to reproduce our experiments, which is a
basic requirement for all published scientific work cryst
thxthxthx to all the day and night owls for the many copies
The winners have been selected, no more entries needed.
thx again br
-Original Message-
From: Miriam Hirshberg [mailto:[EMAIL PROTECTED] On Behalf Of Miriam
Hirshberg
Sent: Thursday, August 16, 2007 1:58 PM
To: Bernhard Rupp
my nature web connection just died for good (probably a preventive
measure..)
Could someone kindly email me the pdfs of the comment and response?
Thx br
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
[EMAIL PROTECTED]
[EMAIL PRO
The deposited structure 2HR0 shows all the signs of having been refined,
deliberately or accidentally, against 'calculated' data. The model used
to 'calculate' the data had (almost) constant B-values in a rather empty
cell containing no solvent. For example, it could have been a (partial?)
molec
I like to emphasize that the infamous table 1 alone should
have immediately tipped off any competent reviewer.
The last shell I/Isig is 1.3 and rmerge 0.11 (!). Rfree and R
have extraorinarily low gaps. And all that for a
large, porportedly flexible multidomain molecule.
Enough to ask more questio
Dear All,
Without passing any judgement on the veracity of C3b structure 2hr0, I
note that the Ca RMSD of this structure with C3 structure 2a73 was
unusually low, compared to the RMSD of 2a73 to the related entries 2a74
and 2i07 by the same group, bovine C3 structure 2b39 and C3b and C3c
structure
Perhaps the most frequent topic of discussion that I have seen
consistently arising in my recent conversations with drug discovery
researchers, is the topic of Virtual Screening and its complexities,
confusions, and varying validity and reliability. John Irwin and I
initiated the idea of a bes
Dear all,
using refmac5 to provide H-atoms for a protein structure the
distance between CYS-CG and HG is defined to 1.34 Ang. in CYS.cif.
That distance has been mentioned by a non-CCP4 program
by
* Poor covalent bond length of 1.33954 for hydrogen atom
In an other library-file CSH.cif the sa
PS I wasn't aware Nature now requires structure factors to be
submitted - which breaks down one of my arguments...
I still hope the authors provide the images though, otherwise I will
start suspecting much more structure than I do now.
In the meantime, all for required submission of raw images,
Hello All,
This debacle is actually quite reminiscent of a similar incident that Wayne
Hendrickson caught in
the 1970's concerning purported "tRNA crystals." Turned out to be completely
fabricated, and the
guy's career went down the drain, I think. A good example to tell your trainees.
Jacob Ke
On Thu, 16 Aug 2007, Kay Diederichs wrote:
Date: Thu, 16 Aug 2007 17:16:54 +0200
From: Kay Diederichs <[EMAIL PROTECTED]>
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The importance of USING our validation tools
I'm glad that the discussion has finally set in, and would only like to
comment
The pdb will give the depositor the results of their validation runs and
identify problems - however they cannot force depositors to address those
problems...
J
Gina Clayton <[EMAIL PROTECTED]> wrote:>
> I thought that when a structure is deposited the databank does run its
> own
> refinement v
On Thu, Aug 16, 2007 at 03:13:29PM +0100, Phil Evans wrote:
> What do you count as raw data? Rawest are the images - everything
> beyond that is modellling - but archiving images is _expensive_!
Maybe we should contact Google to let them do it for us ;-)
http://news.bbc.co.uk/2/hi/technolog
I think the average structure is much less than 20 GB since most data
seems to be collected as SAD. I quickly looked at my data ~20
structures 3 MAD, 9 SAD, 3 MIR, 4 MR, number of amino acids per asu 150
- 9600, the average was closer to 3 GB (compressed). The largest dataset
24 GB (compressed
This structure (1h6w) provides an interesting comparison; it looks just
as I would expect though for such an interesting extended fold.
There are big peaks on the 3-fold axis; there is wispy density which
would be very hard to model - I found an ILE in the wrong rotamer (341A)
- (there is ALWAYS
Ashley Buckle wrote:
By raw data I mean images. We think this is only manageable using a
distributed data grid model (eg Universities/institutions setup their
own repositories using open standards, and PDB aggregate the links to
them. URL persistence will be a hurdle I admit).
This reminded
For nice crystals data processing is straightforward. For crystals with
large unit cells, high mosaicity, and diffuse scattering, processing
can be critical. It may be that future advances in integration
software will allow one to extract far better data from such a
diffraction dataset than can be
Refmac will not introduce a repulsion unless the sum of the occupancies
of the two neighbouring atoms id > 1.00 . Is that the case for you? ( It
might list the close contacts - but shouldnt use them)
If you want a link between the ligand and something else though you must
label them both A or B
I'm glad that the discussion has finally set in, and would only like to
comment on the practicability of storing images.
Mischa Machius schrieb:
I don't think archiving images would be that expensive. For one, I have
found that most formats can be compressed quite substantially using
simple, s
Validation aside, access to raw data is also helpful for method
development (eg integration and scaling algorithms), on which we all
rely.
Ashley
On 17/08/2007, at 1:04 AM, Santarsiero, Bernard D. wrote:
Sorry, I think it's a waste of resources to store the raw images. I
think
we should tr
On Thu, Aug 16, 2007 at 03:13:29PM +0100, Phil Evans wrote:
> What do you count as raw data? Rawest are the images - everything
> beyond that is modellling - but archiving images is _expensive_!
Hmmm - not sure: let's say that a typical dataset requires about 180
images with 10Mb each image. W
On Aug 16, 2007, at 15:22, Randy J. Read wrote:
Raw images are probably even harder to simulate convincingly.
If i was to fabricate a structure, I would get first 'Fobs', then
expand, then get the images
(I am sure one can hack 'strategy' or 'predict' or even 'mosflm' to
tell you in which
Dear all,
With regards to the possible "fabrication" of the 2hr0 structure, why
would the authors have deposited the structure factors if this is not
required by the journal? Also, why would they have "fabricated" a
structure with gaps along c if they could have done so without the gap?
I
Hello all,
I started to write a response to this thread yesterday. I thought the title was
great even the content of Eleanor's email was very helpful. What I didn't like
was the indictment in the next to last paragraph. This has been followed up
with the word fabrication by others. No one knows
Dear all,
I am refining a structure with a partially
occupied ligand. The binding site contains a
Glutamine residue with a dual conformation with
the B conformation overlapping with the ligand.
I have named the ligand ALIG but when refining,
Refmac notes a number of VDW deviations and th
Sorry, I think it's a waste of resources to store the raw images. I think
we should trust people to be able to at least process their own data set.
Besides, you would need to include beamline parameters, beam position,
detector distances, etc. that may or may not be correct in the image
headers. I'
Hmm - I think I miscalculated, by a factor of 100 even!... need more
coffee. In any case, I still think it would be doable. Best - MM
On Aug 16, 2007, at 9:30 AM, Mischa Machius wrote:
I don't think archiving images would be that expensive. For one, I
have found that most formats can be com
I don't think archiving images would be that expensive. For one, I
have found that most formats can be compressed quite substantially
using simple, standard procedures like bzip2. If optimized, raw
images won't take up that much space. Also, initially, only those
images that have been used
By raw data I mean images. We think this is only manageable using a
distributed data grid model (eg Universities/institutions setup their
own repositories using open standards, and PDB aggregate the links to
them. URL persistence will be a hurdle I admit). You are right in
that a single-rep
What do you count as raw data? Rawest are the images - everything
beyond that is modellling - but archiving images is _expensive_!
Unmerged intensities are probably more manageable
Phil
On 16 Aug 2007, at 15:05, Ashley Buckle wrote:
Dear Randy
These are very valid points, and I'm so gla
Dear Randy
These are very valid points, and I'm so glad you've taken the
important step of initiating this. For now I'd like to respond to one
of them, as it concerns something I and colleagues in Australia are
doing:
The more information that is available, the easier it will be to
dete
Dear all,
I've got a question regarding NSCM keyword usage in MolRep. If I am
searching for a trimer in the ASU, but I use a monomer as model, should I
put NSCM=3 or =1?
Thanks,
Cynthia.
I believe that is so.
In this case the Rfactor against the deposited data is low. The question
to be addressed is whether the deposited data is of acceptable quality.
There are some poor distances but not many - the asymmetric unit is very
empty.
The Ramachandran plot is not good, and an autho
On Aug 16 2007, Eleanor Dodson wrote:
The weighting in REFMAC is a function of SigmA ( plotted in log file).
For this example it will be nearly 1 for all resolutions ranges so the
weights are pretty constant. There is also a contribution from the
"experimental" sigma, which in this case seems
I thought that when a structure is deposited the databank does run its own
refinement validation and geometry checks and gives you back what it finds i.e
distance problems etc and rfactor?
Quoting Eleanor Dodson <[EMAIL PROTECTED]>:
The weighting in REFMAC is a function of SigmA ( plotted in l
Not enough information but some suggestions.
Are you sure the data is OK? Any sign of twinning? That is suspicious
if you cant decide between P43 and P43212
(Run SFCHECK on the amplitudes and try to understand output! )
Or send it and I will provide commentary.
Eleanor
Yanming Zhang wrote:
Dear Elisabetta,
from the statistics you attach it seems that your low resolution extends only
to 6.72 A
My guess is that if you could include as much low resolution as possible (e.g.
up to 20A or more)it will help a lot in getting better maps etc.,
I hope this is the answer you are looking
What does the matthews_coeff indicate? You would expect more water than
that, but maybe you have a low Matthews_coeff indicating little solvent?
maybe you have lost the low resolution data which makes it harder to
find water? Maybe you have refined with bulk solvent scaling -
sometimes that
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